Aneuploidy of the sex chromosomes is common among recognized congenital syndromes. For example, the majority (80%) of individuals with Klinefelter syndrome have 2 X chromosomes and 1 Y chromosome; the remainder are mosaics or variants. Individuals with Turner syndrome have a single X chromosome in 55% of cases; the remaining 45% are either variants or mosaics.

Specimens that contain >5% cells with a signal pattern other than XX in females and XY in males have a very high likelihood of having a clone of cells with an abnormal complement of sex chromosomes.

Specimens with <5% of cells with a signal pattern other than XX in females and XY in males most likely do not have a clone of cells with an abnormal complement of sex chromosomes, but the presence of an abnormal clone of cells is not completely ruled out.

Conventional cytogenetic analysis should be performed for confirmation, especially when the results are abnormal.

Structural abnormalities of X and Y chromosomes will be missed by this technique, as will low-level mosaicism.

This test can detect between 50% to 70% of Turner syndrome cases (only those caused by complete lack of 1 sex chromosome [45,X] or high-level mosaicism for a 45,X). Congenital blood chromosome analysis (CMS / Chromosome Analysis, for Congenital Disorders, Blood) should always be performed for Turner syndrome.

The test does not rule out numeric or structural cytogenetic anomalies involving chromosomes other than X and Y.